Abstract Summary: Proteins can adopt a variety of conformations. We present a simple server for scoring the agreement between 3D atomic structures and experimental envelopes obtained by atomic force microscopy. Three different structures of immunoglobulins (IgG) or blood coagulation factor V activated were tested and their agreement with several topographical surfaces was computed. This approach can be used to test structural variability within a family of proteins. Availability and implementation: DockAFM is available at http://biodev.cea.fr/dockafm. Contact: [email protected] or [email protected] Supplementary information: Supplementary data are available at Bioinformatics online.

Summary: Improving and ascertaining the quality of a multiple sequence alignment is a very challenging step in protein sequence analysis. This is particularly the case when dealing with sequences in the ‘twilight zone’, i.e. sharing <30% identity. Here we describe INTERALIGN, a dedicated user-friendly alignment editor including a view of secondary structures and a synchronized display of carbon alpha traces of corresponding protein structures. Profile alignment, using CLUSTALW, is implemented to improve the alignment of a sequence of unknown structure with the visually optimized structural alignment as compared with a standard multiple sequence alignment. Tree-based ordering further helps in identifying the structure closest to a given sequence. Availability: Windows and Linux packages, as well as source files, are available under the CeCILL free software licensing agreement at the following address: http://www-dsv.cea.fr/content/cea/d_dep/d_diep/d_sbtn/download.htm Contact:[email protected]